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From what I can understand both are largely uncompressed formats, but whats the difference between the two? Normally I just use MP3 for the size but an audio project I'm going to be working on (the final product being a CD) so it would be interesting and useful to know what is the best to work with.

FLAC is a format which can be compressed by design to take up less space should you want to, Wave on the other hand can not. Both formats are lossless, but encoding a compressed FLAC file takes more time than the non-compressible Wave file format.

Personally I would most likely use Wave while editing unless storage space is a scarcity.

What Minox said although I will note many of the fancier audio editing programs (and if you are going to master it properly then you will probably run into one) prefer wave input so definitely that when playing audio engineer.

For reference CD effectively uses wave and at CD samplerates (48KHz) a stereo track runs what 80 minutes per CD (or 74 if you are cheap) or about 700 megs (out the several hunder gigs I imagine you have at your disposal) so it is not like you are working with uncompressed video which does still take up enough space to have to worry about it.

Anything more and I will probably have to don my audio engineer hat which would be better served by linking up